5Y7T | pdb_00005y7t

Quaternary complex of AsqJ-Fe3+-2OG-D-cyclopeptin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 
    0.238 (Depositor), 0.241 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Insights into the Desaturation of Cyclopeptin and its C3 Epimer Catalyzed by a non-Heme Iron Enzyme: Structural Characterization and Mechanism Elucidation.

Liao, H.J.Li, J.Huang, J.L.Davidson, M.Kurnikov, I.Lin, T.S.Lee, J.L.Kurnikova, M.Guo, Y.Chan, N.L.Chang, W.C.

(2018) Angew Chem Int Ed Engl 57: 1831-1835

  • DOI: https://doi.org/10.1002/anie.201710567
  • Primary Citation Related Structures: 
    5Y7R, 5Y7T

  • PubMed Abstract: 

    AsqJ, an iron(II)- and 2-oxoglutarate-dependent enzyme found in viridicatin-type alkaloid biosynthetic pathways, catalyzes sequential desaturation and epoxidation to produce cyclopenins. Crystal structures of AsqJ bound to cyclopeptin and its C3 epimer are reported. Meanwhile, a detailed mechanistic study was carried out to decipher the desaturation mechanism. These findings suggest that a pathway involving hydrogen atom abstraction at the C10 position of the substrate by a short-lived Fe IV -oxo species and the subsequent formation of a carbocation or a hydroxylated intermediate is preferred during AsqJ-catalyzed desaturation.


  • Organizational Affiliation
    • Institute of Biochemistry and Molecular Biology, College of Medicine, National (Taiwan) University, Taipei, 100, Taiwan.

Macromolecule Content 

  • Total Structure Weight: 35.47 kDa 
  • Atom Count: 2,344 
  • Modeled Residue Count: 287 
  • Deposited Residue Count: 315 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Iron/alpha-ketoglutarate-dependent dioxygenase asqJA [auth B]315Aspergillus nidulans FGSC A4Mutation(s): 0 
Gene Names: asqJAN9227
EC: 1.14 (PDB Primary Data), 1.14.11.81 (UniProt)
UniProt
Find proteins for Q5AR53 (Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139))
Explore Q5AR53 
Go to UniProtKB:  Q5AR53
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5AR53
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free:  0.238 (Depositor), 0.241 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.471α = 90
b = 118.619β = 90
c = 66.427γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2018-01-24 
  • Deposition Author(s): Liao, H.J.

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-24
    Type: Initial release
  • Version 1.1: 2018-01-31
    Changes: Database references
  • Version 1.2: 2018-02-07
    Changes: Database references
  • Version 1.3: 2018-02-21
    Changes: Database references
  • Version 1.4: 2024-03-27
    Changes: Data collection, Database references, Derived calculations